Measuring microbiome disruption

How should doctors measure how messed up someoneâ€™s intestinal microbiome is?

This is the topic of a recent paper in American Journal of Infection Controlfrom Colleen Kraft and colleagues from Emory and the Centers for Disease Control and Prevention. The corresponding author is epidemiologist Alison Laufer Halpin at the CDC.

What the authors are moving towards is similar to Shannonâ€™s index, which ecologists use to measure diversity of species. Another way to think about it is like the Gini coefficient, a measure of economic inequality in a country. If there are many kinds of bacteria living in someoneâ€™s body, the disruption index should be low. If there is just one dominant type of bacteria, the disruption index should be high.

In the paper, the authors examined samples from eight patients in a long-term acute care hospital (Wesley Woods) who had recently developed diarrhea. Using DNA sequencing, they determined what types of bacteria were present in patients’ stool. The patientsâ€™ samples were compared with those from two fecal microbial transplant donors.

Long-term acute care hospital patients tend to have high antibiotic consumption. In some patients, multiple rounds of antibiotics can lead to colonization by harmful, drug-resistant bugs such as Clostridium difficile, vancomycin-resistant enterococci (VRE) or carbapenem-resistant Enterobacteriaceae (CRE). To some extent, the authors were able to correlate patientsâ€™ antibiotic treatment history with their microbial diversity or lack of it. They say that measures of microbiome diversity should assess several factors:

*Overall diversity â€“ how much does one type of bacteria dominate

*Presence of bad guys, such as those mentioned above

*Presence of â€œkeystoneâ€ species that prevent takeover by the bad guys

*Presence of bacteria thought to be beneficial or protective, such as Barnesiella or F. prausnitzii, but not necessarily the same as keystone species